Open ayoraind opened 4 months ago
I just did a quick check by running the bash script outside the Nextflow pipeline, with or without the --keep_fastqs
argument. Plassembler ran successfully, and showed that there at least 2 circularized plasmids
>1 length=263626 plasmid_copy_number_short=1.04x plasmid_copy_number_long=1.14x
>2 length=43380 plasmid_copy_number_short=0.75x plasmid_copy_number_long=0.47x circular=true
>3 length=42020 plasmid_copy_number_short=1.4x plasmid_copy_number_long=1.36x
>4 length=13841 plasmid_copy_number_short=4.31x plasmid_copy_number_long=1.79x circular=true
>5 length=11136 plasmid_copy_number_short=1.03x plasmid_copy_number_long=0.62x
So, I think it has something to do with my Nextflow pipeline.
I found the cause of the error. The error occured only when I set the argument -m
to 1. If -m
is not specified (default is 500), the pipeline runs successfully. Is it possible to make the run continue with a warning message in the logs rather than stopping altogether (for the sake of Nextflow/Snakemake)?
Hi @ayoraind ,
Thanks so much for this detailed bug report - I'll put in a fix soon for sure (probably will just skip all really short reads that seemingly cause this issue)
George
Hi @gbouras13,
Thank you very much.
Hi @gbouras13,
Many thanks for your excellent tool. I am trying to implement Plassembler (v1.6.2) within one of my in-house Nextflow pipelines on a Linux machine. Plassembler analysis ran successfully for one of two genomes of interest. For the second genome, Plassembler stopped at the
processing Sam/Bam Files and extracting Fastqs
step. Kindly find the error message below.The bash command;
My guess is that there are no fastqs to be extracted by Plassembler (using the
--keep_fastqs
argument). Is this correct? If so, does this mean that no plasmids are present in this genome? If truly there are no plasmids, is it then possible that an empty fastq file (e.g., within the plasmid_fastqs directory) is produced and the run continues with a warning message in the logs rather than stopping altogether (thinking Nextflow/Snakemake application)?